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Patrick Cherry
PhD scientist skilled in data visualization, statistical modeling, bioinformatics, biological data science, next-generation sequencing (NGS), and tool-building. I’ve coded reproducible and rigorous pipelines for high-throughput experimental designs and multi-omic analyses for communication to technical and non-technical audiences. I’ve launched best-in-class oncology reference standards, and invented new molecular methods for DNA and microbe manipulation. Originally trained in Molecular Biology, I am passionate about advancing data science and bioinformatics to improve human health.
Education
PhD
University of Colorado School of Medicine
Aurora/Denver, Colorado
2019 - 2013
- Ph.D. in Molecular Biology
- Advisor: Jay Hesselberth, PhD.
- Thesis: RNA Terminus chemistry affects the decay events that target HAC1 mRNA during the Unfolded Protein Response
BA
Hendrix College
Conway, Arkansas
2013 - 2009
- Biochemistry and Molecular Biology, with Distinction
- Advisor: Andres Caro, PhD. Senior Capstone Project showing key stress response gene expression changes to oxidative stress in liver cells
- Minor in Mathematics; PI: Lars Seme; Project: Newton’s method as a fractal chaotic dynamical system
Industry Experience
I currently split my time between wet lab and computational activities. I have worked in a variety of roles ranging from HTP strain onboarding to genomics scientist. I like collaborative environments where I can learn from my peers and in turn teach others.
Senior Scientist, Genomics
Twist Bioscience
South San Francisco, California
Current - 2022
- Tech Lead of multiple NPIs and custom OEMs; invented and launched products to yield millions of dollars in new revenue, including: Pan-cancer cfDNA (v1 & v2), CNV Controls, RNA Fusion Controls, Fragmentome Controls, and RNA-seq
- Built positive team culture; mentored and promoted a report from Senior Research Associate to Scientist; coached reports who served as Tech Leads on new product introductions, increasing revenue. Delivered quality science on deadline by managing research assistants
- Original research and presentations unveiled novel products and underwrote multiple patents for product configuration and biochemical approaches. Gained new customers in RNA standards space with the design and implementation of high-throughput RNA synthesis and pooling
- Analyzed public databases and feedback from alpha testers to optimize design of multiple products; routinely craft custom data analysis pipelines in R and Python; documented analyses using
Rmarkdown,Quarto, andJupyter; maintain git repo of dockerized bioinformatic QC packages for Pan-cancer cfDNA product line - Generated actionable data for new technology evaluations of a new NGS platform with custom experiments and bioinformatic analyses in Python, R, and SQL to enable faster gene QC in Production. Launched a time-saving gene synthesis change into production, supported by original experimental data. Boosted colleagues in publication-ready plots by coding and distributing on company GitHub the internal package
twistcolorpal, which automatically styles plots and sets up database connectors toSQL/ Snowflake for parameterizeddbplyrquerying. Regularly use R, tidyverse, Python, Polars, AWSs3,Spark,PySpark, andSparklyr, locally and on Databricks. Regularly implements and runs automated code tests
Scientist, Genomics
Twist Bioscience
South San Francisco, California
Current - 2021
- Tech Lead of Pan-Cancer Reference Standard, an ISO-13485 synthetic positive control with 458 unique variants among 84 cancer-associated genes at six QC’d VAFs, plus a WT control; launched in Nov of 2021
- Invented, validated, and deployed to production multiple widely-used primer removal methods for DNA standards and high-complexity synthetic dsDNA pools
- Devised and validated precise high-throughput DNA quantification process for accurate pooling. On-boarded droplet digital PCR (ddPCR) system into production; designed and validated custom ddPCR assays for use in production
- Led multiple iterations of custom NGS analysis; refined the QC approach and thresholds for ensuring a contamination-free production process; extensively used data visualization to communicate complex data to cross-functional teams
- Made extensive use of UMI sequencing and created novel method to rigorously quantify library conversion efficiency to evaluate products and reference materials
Scientist I, NGS & NPI-Build
Zymergen, Inc.
Emeryville, California
2021 - 2019
- Achieved a 95% success rate for obtaining a genetic edit by designing and implementing multiple automated high-throughput methods for a non-model microbe: transformation, counterselection, and NGS genotyping
- Determined best methods for genetic manipulation, propagation, and archiving of a non-model microbe through design & execution of complex experiments on lab automation with and without LIMS sample tracking
- Boosted NGS core genotyping success by 45% using data-driven decision making and teaching; guided demanding and diverse internal customers on complex NGS experiments
- Applied statistical methods to screen and optimize a genetic engineering protocol for newly-on-boarded microbe; delivered robust process while working on New Product Introduction team
- Delivered on microbe improvement KPIs by designing and building hundreds of plasmids using modern molecular techniques like Gibson and Golden Gate
Research Experience
I worked on a few projects during my PhD, and the RNA repair project led me to custom 5’-OH RNA-seq libraries, which inspired my fascination with transcriptomics and bioinformatics.
Doctoral Research
University of Colorado School of Medicine
Aurora/Denver, Colorado
2019 - 2014
- Wrote, revised, & published two academic papers on RNA repair & yeast genetics
- Engineered and characterized genetic bypass of essential genes in budding yeast; on-boarded CRISPR/Cas9 for efficient and precise gene knock-in
- Expressed, purified, and used wild-type and mutant recombinant protein in E. coli to carry out an RNA modification enzymatic assay
- Optimized custom RNA-seq library protocol; independently planned, executed, troubleshooted RNA modification detection
- Routinely conducted northern blotting, targeted depletion, primer extension, splinted ligation, and other esoteric DNA and RNA experiments
Undergraduate Research Assistant
Lab of Dr. Andres Caro, Hendrix College
Conway, Arkansas
2013 - 2012
Summer Undergraduate Research Fellowship
Lab of Dr. Michael Shiloh, UT Southwestern Medical Center
Dallas, Texas
2012 - 2012
Research Assistant
Lab of Dr. Joy Sturtevant, Louisiana Health Sciences Center
New Orleans, Louisiana
2011 - 2010
Intellectual Property
Working at Twist and Zymergen on new product research requires confidentiality, but public evidence of accomplishments often comes in patent applications. The Legal teams know me well for being a helpful expert in the process.
Methylation-mediated adapter removal on nucleic acid sequences
Twist Bioscience
South San Francisco, California
3/7/23
- US 63/317,466
Expansion of cfDNA for Libraries
Twist Bioscience
South San Francisco, California
11/12/21
- US Prov. Pat. Ref No 823.102
Libraries for mutational analysis
Twist Bioscience
South San Francisco, California
4/9/21
- US Prov. Pat. Ref No 823.101
Method for counterselection in microorganisms
Zymergen, Inc.
Emeryville, California
3/25/21
- US 2021_0087586 A1
Selected Publications
I communicate my results clearly, both in writing and in live presentations. I enjoy writing research papers, but my career has required more tech notes and app notes recently.
Characteristics and specificity of the wild-type / 0% VAF reference material
Twist Bioscience
South San Francisco, California
4/22/22
- Patrick Cherry & Mike Bocek
Twist Pan-cancer synthetic reference materials technical guide
South San Francisco, California
12/21/21
- Patrick Cherry & Mike Bocek
Multiple decay events target HAC1 mRNA during splicing to regulate the unfolded protein response
N/A
2019
- Cherry, P., Peach, S., & Hesselberth, J.
Genetic bypass of essential RNA repair enzymes in budding yeast
N/A
2018
- Cherry, P., White, L., York, K., & Hesselberth, J.
Selected Presentations & Talks
I give audience-centered presentations by adapting on the fly and over time to the venue and occasion. I like to transfer knowledge by giving methods/best practices talks whose slides can also serve as documentation.
Twist pan-cancer reference standard V2: Enhanced precision and reduced errors in ctDNA analysis
Advances in Genome Biology and Technology
Orlando, Florida
2/6/24
- Lydia Bonar, Patrick Cherry, Michael Bocek, Shawn Gorda, Derek Murphy, and Esteban Toro
High sensitivity detection of specific ultra low-frequency somatic mutations for minimal residual disease (MRD) monitoring
International Society of Liquid Biopsy Annual Congress
Madrid, Spain
11/19/23
- Tina Han, Tong Liu, Michael Bocek, Patrick Cherry, Shawn Gorda, Nairi Pezeshkian, Dan Nasko, Po-Yuan Tung, Derek Murphy, and Esteban Toro
Twist pan-cancer synthetic RNA fusion control for assay development
American Association for Cancer Researchers
Orlando, Florida
4/16/23
- Patrick Cherry, Jason Corwin, Yu Cai, Kit Fuhrman, Jean Challacombe, Derek Murphy, Esteban Toro
High sensitivity detection of specific ultra low-frequency somatic mutations for minimal residual disease (MRD) monitoring
American Association for Cancer Researchers
Orlando, Florida
4/19/23
- Tong Liu, Michael Bocek, Patrick Cherry, Shawn Gorda, Jean Challacombe, Derek Murphy and Esteban Toro
An end-to-end workflow for accurate methylation detection
American Association for Cancer Researchers
Orlando, Florida
4/19/23
- Lydia Bonar, Kristin Butcher, Michael Bocek, Holly Corbitt, Bryan Hoglund, Cibelle Nassif, Patrick Cherry, Derek Murphy, Jean Challacombe, Esteban Toro
Colorado RNA Club Industry Session
Colorado RNA Club
Boulder, Colorado
4/10/23
Use of synthetic CNV fragments to mimic copy number alterations for ctDNA reference standards
Advances in Genome Biology and Technology
Hollywood, Florida
2/7/23
- Jason Corwin, Patrick Cherry, Shawn Gorda, Michael Bocek, Jean Challacombe, Derek Murphy, Esteban Toro
Methylation Controls to detect for methylation level quantification in the Twist Targeted Methylation Sequencing workflow
Advances in Genome Biology and Technology
Hollywood, Florida
2/7/23
- Kristin Butcher, Michael Bocek, Patrick Cherry, Jean Challacombe, Esteban Toro
Efficient, high sensitivity detection of oncogenic variants with UMIs and target enrichment
European Human Genetics Conference
Vienna, Austria
5/26/22
- Michael Bocek, Lydia Bonar, Jean Challacombe, Richard Gantt, Patrick Cherry, Rebecca Liao, Derek Murphy and Esteban Toro
Twist pan-cancer synthetic reference materials for cell-free DNA (cfDNA) assay development
American Association for Cancer Researchers
New Orleans, Louisiana
4/12/22
Twist reference material products: current methods and future applications
Twist R&D Symposium
South San Francisco, CA
3/17/22
Pan-cancer Reference Standard: Methods in Automation & Future Needs
Twist Automation Group Meeting
South San Francisco, CA
4/5/22
Pan-cancer Reference Standard: Methods & Lessons from NPI & QC
Twist R&D Meeting
South San Francisco, CA
2/15/22
Molecular Methods Meet the Standards: Or how I learned to stop worrying and love UV-quantification
Twist R&D Meeting
South San Francisco, CA
7/13/21
R use at Zymergen
Z-Tech Talk
Emeryville, CA
6/16/20
Data-driven troubleshooting of NGS experiments
Data Science Talk
Emeryville, CA
4/20/20
NGS Sample Preparation Deep-Dive
NGS Technical Talk Series
Emeryville, CA
3/27/20
Colorado RNA Club Industry Session
Colorado RNA Club
Boulder, Colorado
4/10/21
RNA terminus chemistry potentiates decay events that target HAC1 mRNA during the unfolded protein response
Thesis Defense Seminar
Aurora, Colorado
2019
RNA modification and decay regulates the unfolded protein response
Rocky Mountain Yeast Meeting Poster
Fort Collins, Colorado
2019
What the unfolded protein response teaches us about RNA decay
Bolie Scholar Talk, Molecular Biology Program Retreat
Winter Park, CO
2018
Genetic bypass of essential yeast RNA repair enzymes
Rocky Mountain Yeast Meeting Poster
Golden, Colorado
2018
RNA processing regulates the unfolded protein response
CSHL: mRNA Processing Meeting Talk
Cold Spring Harbor, New York
2017
Genetic bypass of essential yeast RNA repair enzymes
Molecular Biology Program Update Talk
Aurora, Colorado
2017
Genetic bypass of essential yeast RNA repair enzymes
Rocky Mountain Yeast Meeting Poster
Boulder, Colorado
2017
RNA processing regulates the unfolded protein response
RNA Club Talk
Boulder, Colorado
2016
RNA Healing and Destruction
Molecular Biology Program Update Talk
Aurora, Colorado
2016
RNA processing regulates the unfolded protein response
Rocky Mountain Yeast Meeting Poster
Fort Collins, Colorado
2016
Turnover of endonucleolytic products of No-Go mRNA decay
RNA Stability Meeting
Estes Park, Colorado
2015
RNA 5?-kinase-mediated co-translational mRNA decay
Molecular Biology Program Update Talk
Aurora, Colorado
2015
RNA 5?-kinase-mediated co-translational mRNA decay
Rocky Mountain Yeast Meeting Poster
Aurora, Colorado
2015
RNA 5?-kinase-mediated co-translational mRNA decay
Rocky Mountain Yeast Meeting Poster
Boulder, Colorado
2014
Coordinated upregulation of antioxidant protection and mitochondrial DNA biosynthesis in liver cells by oxidative stress
Senior Undergraduate Capstone Research Talk
Conway, Arkansas
2013
Trainees & Direct Reports
While I’ve not held a role with a “manager” title, all Scientist positions I’ve accepted have had formal report management responsibility. I take managing and mentoring seriously and emphasize trust, learning, and growth with my reports.
Derek Cai, BS, University of California San Diego, Research Associate I
Twist Bioscience
South San Francisco, California
Current - 2022
Lydia Bonar, MS, Johns Hopkins University, Scientist
Twist Bioscience
South San Francisco, California
Current - 2021
Alonzo Lee, BS, University of California Santa Cruz, Scientist
Twist Bioscience
South San Francisco, California
2022 - 2021
Kaisle Hill, BA, University of California Berkeley, Senior Research Associate
Zymergen, Inc.
Emeryville, California
2021 - 2020
Rachel A Jones, MS, University of Arizona, Postdoctoral Fellow
University of Colorado School of Medicine
Aurora/Denver, Colorado
2017
Laura K White, MS, Biotechnology, Johns Hopkins University, Postdoctoral Fellow
University of Colorado School of Medicine
Aurora/Denver, Colorado
2016
Haven Himmighoefer, Undergraduate, University of Colorado Denver
University of Colorado School of Medicine
Aurora/Denver, Colorado
2016 - 2014
Leslie Aranda, Undergraduate, University of California Riverside
University of Colorado School of Medicine
Aurora/Denver, Colorado
2015